A Flexible Protein Structure Alignment Method Based on the Residue-Residue network comparison

• Project/Area Number: 26730151
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Life / Health / Medical informatics
• Research Institution: Kitasato University
• Principal Investigator: Terashi Genki 北里大学, 薬学部, 講師 (40383658)
• Project Period (FY): 2014-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000); Fiscal Year 2016: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000); Fiscal Year 2015: ¥130,000 (Direct Cost: ¥100,000、Indirect Cost: ¥30,000); Fiscal Year 2014: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: タンパク質立体構造 / 立体構造アライメント / 構造比較 / タンパク質三次元構造 / 構造アライメント / タンパク質間相互作用 / アミノ酸残基間ネットワーク / アミノ酸残基 / 残基幹ネットワーク / 残基間ネットワーク

Outline of Final Research Achievements

In this project, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. Our novel algorithm can identify homologous relationships at the residue level between related protein structures.
The software is freely available to academic users as stand-alone software at http://www.pharm.kitasato-u.ac.jp/bmd/bmd/Publications.html.

Research Products

• [Journal Article] CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area (2015)
  • Author(s): Genki Terashi, Mayuko Takeda-Shitaka
  • Journal Title: PLoS ONE Volume: 10 Issue: 10 Pages: e0141440-e0141440
  • DOI: 10.1371/journal.pone.0141440
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] CAB-align: Novel protein structure alignment method based on the residue-residue contact area (2016)
  • Author(s): Genki Terashi, Daisuke Kihara, Mayuko Takeda-Shitaka
  • Organizer: ISMB2016 satellite meeting, 3DSIG 2016
  • Place of Presentation: 米国フロリダ州オーランド
  • Year and Date: 2016-07-08
  • Int'l Joint Research
• [Presentation] Flexible protein structure alignment method based on the residue-residue interaction (2015)
  • Author(s): Genki Terashi, Mayuko Takeda-Shitaka
  • Organizer: Great Lakes Bioinformatics Conference 2015
  • Place of Presentation: Purdue University, West Lafayette, Indiana, U.S
  • Year and Date: 2015-05-18
  • Int'l Joint Research
• [Presentation] 残基間相互作用に基づく新たなタンパク質構造アライメント法の開発 (2014)
  • Author(s): 寺師玄記
  • Organizer: 第42回構造活性相関シンポジウム
  • Place of Presentation: 熊本県熊本市 くまもと森都心プラザ
  • Year and Date: 2014-11-14
• [Presentation] Novel protein structure alignment method based on the inter-residue contact area (2014)
  • Author(s): 寺師玄記
  • Organizer: JSBi2014・第3回生命医薬情報学連合大会
  • Place of Presentation: 宮城県仙台市 仙台国際センター
  • Year and Date: 2014-10-02 – 2014-10-04
• [Remarks] 研究成果プログラムCAB-alignの公開ページ
  • URL: http://www.pharm.kitasato-u.ac.jp/bmd/bmd/Download_files/CABalign/